NAME
cnvkit_diagram - Draw copy number (log2 coverages, segments) on chromosomes as a diagram.
If both the raw probes and segments are given, show them side-by-side on
each chromosome (segments on the left side, probes on the right side).
DESCRIPTION
usage: cnvkit.py diagram [-h] [-s SEGMENT] [-c CHROMOSOME] [-t THRESHOLD]
- [-m MIN_PROBES] [-y]
-
[-x {m,y,male,Male,f,x,female,Female}] [--no-shift-xy] [-o FILENAME] [--title TITLE] [--no-gene-labels] [filename]
positional arguments:
- filename
-
Processed coverage data file (*.cnr), the output of the 'fix' sub-command.
options:
- -h, --help
-
show this help message and exit
- -s SEGMENT, --segment SEGMENT
-
Segmentation calls (.cns), the output of the 'segment' command.
- -c CHROMOSOME, --chromosome CHROMOSOME
-
Chromosome to display, e.g. 'chr1' (no chromosomal range allowed)
- -t THRESHOLD, --threshold THRESHOLD
-
Copy number change threshold to label genes. [Default: 0.5]
- -m MIN_PROBES, --min-probes MIN_PROBES
-
Minimum number of covered probes to label a gene. [Default: 3]
- -y, --male-reference, --haploid-x-reference
-
Assume inputs were normalized to a male reference (i.e. female samples will have +1 log-CNR of chrX; otherwise male samples would have -1 chrX).
- -x {m,y,male,Male,f,x,female,Female}, --sample-sex {m,y,male,Male,f,x,female,Female}, -g {m,y,male,Male,f,x,female,Female}, --gender {m,y,male,Male,f,x,female,Female}
-
Specify the sample's chromosomal sex as male or female. (Otherwise guessed from X and Y coverage).
- --no-shift-xy
-
Don't adjust the X and Y chromosomes according to sample sex.
- -o FILENAME, --output FILENAME
-
Output PDF file name.
Plot aesthetics:
- --title TITLE
-
Plot title. [Default: sample ID, from filename or -i]
- --no-gene-labels
-
Disable gene_name labels on plot (useful when a lot of CNV were called).